8I66

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with isoorotic acid (2,4-Dihydroxypyrimidine-5-carboxylic Acid) and citric acid, Form I

PDB DOI: https://doi.org/10.2210/pdb8I66/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-27 Released: 2023-07-12
Deposition Author(s): Raj, P., Paul, A., Gopal, B.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.234
R-Value Work: 0.178
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with the barbituric acid fragment

Kesharwani, S., Raj, P., Paul, A., Roy, K., Bhanot, A., Mehta, A., Gopal, A., Varshney, U., Gopal, B., Sundriyal, S.

(2023) Eur J Med Chem 258: 115604

DOI: https://doi.org/10.1016/j.ejmech.2023.115604

Macromolecule Content

Total Structure Weight: 26.16 kDa
Atom Count: 1,788
Modelled Residue Count: 228
Deposited Residue Count: 238
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A	238	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: ung, Rv2976c, MTCY349.11 EC: 3.2.2.27
UniProt
Find proteins for P9WFQ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFQ9 Go to UniProtKB: P9WFQ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WFQ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
5CU (Subject of Investigation/LOI) Query on 5CU Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid C₅ H₄ N₂ O₄ ZXYAAVBXHKCJJB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.234
R-Value Work: 0.178
R-Value Observed: 0.181
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.12	α = 90
b = 63.97	β = 112.29
c = 45.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	India	--

Revision History (Full details and data files)

Version 1.0: 2023-07-12
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.